Figure 8

The effect of washing on the Hook-curves: In the second series the chips are labeled and stained a second time and subsequently washed using the same protocol as in the first series. Panel b re-plots the hook-curves for chip A (1 st series) together with theoretical functions which were calculated using Eq. (20) for different numbers of washing cycles. Washing first of all increases the width and the height of the hooks. The two trends reflect different effects: The increased width can be attributed to the strong removal of non-specific transcripts whereas the increased height indicates the stronger effect of washing on the MM-probes. Specific transcripts bound to the PM probes are relatively stable against washing as indicated by the virtually invariant right flank of the hook curves. See also Figure 17 below (part a) which assigns the geometrical dimensions of the hook-curve to the parameters used.